title: 207760740056_R05C01


title: CTX Rbfox1 cKO 2

status: Public on May 15 2024

type: SRA

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

country: USA

institute: UCLA

description: Ribosome protected mRNA fragments

library_source: transcriptomic

data_processing:
Sequence reads were demultiplexed using HtSeqTools.
Input sequence reads linkers and adapters were removed with cutadapt.
Reads shorter than 24nt were discarded. Reads were aligned to the mm10 rRNA sequences with bowtie with default parameters and unaligned reads were retained
Reads were then aligned to the mm10 genome using STAR 2.5.4b
Assembly: mm10
Supplementary files format and content: bigwig

molecule: total RNA

organism: Mus musculus

source_name: Cortex E15 DIV14

growth_protocol: E15 Rbfox1 fl/fl primary neuronal cultures were plated on PDLL coated 10cm plates at 5.8E+6 density. Plating media changed to feeding media after 24 hours and fed every 3-5 days thereafter.

extract_protocol:
Cells were harvested at DIV14. each plates was washed with ice-cold PBS containing 100ug CHX, lysed in dish with 400ul lysis buffer, scraped, left for 10minutes, and triturated 5x using a G26 needle.
Library was constructed following the protocol discribed by  Nicholas J. McGlincy and Nicholas T. Ingolia, Methods 2017. (titled: Transcriptome-wide measurement of translation by ribosome profiling)

treatment_protocol: AAV2/9-hSyn-Cre-eGFP or AAV2/9-hSyn-eGFP virus was used to infect cells at DIV3. Approximately 100% infection efficiency.

tag: tissue

value: Cortex E15 DIV14

tag: cell line

value: A0010 TAGCTT

tag: cell type

value: NI-812 CGTAA


title: Placenta_Saline_F_repl1

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: 3' Quant seq with UMI tags

data_processing:
Raw sequencing reads were assessed for quality control using FastQC and multiqc umi indexes were added using umi2index (Lexogen) and then trimmed to remove adapter contamination, polyA read through and low-quality reads using BBDuk.
All samples were then re-assessed for quality using FastQC and multiqc.
Samples were aligned to the mouse genome (mm10) using STAR
Aligned bam files were then filtered for only unique UMIs using collapse_UMI_bam (Lexogen).
Filtered bam files were sorted and indexed using samtools.
Reads per gene were then counted using feature counts at the gene id levels with -s 1 desginated for stranded RNAseq.
Counts were then read into R for statistical analysis using EdgeR and LimmaVoom.
Assembly: mm10
Supplementary files format and content: FeatureCounts counts table in .txt

source_name: placenta

extract_protocol:
5 days following the Poly I:C injection on ED17.5, pregnant dams were euthanized using CO2. The uterine horn was dissected out and placenta and fetal brains were taken from each of the offspring and flash frozen with dry ice. RNA was isolated from fetal brain (n = 32; 16 males and 16 females) and placentas (n = 32; 16 males and 16 females) from 7-8 litters using RNA/DNA Miniprep Plus Zymogen Kit (Cat#D7003). To ensure purity, RNA was further treated with DNAse1 for 15 minutes. RNA quantification was done using a Qubit. Chemical purity was determined using a Nanodrop, where the absorbance ratios fell between 1.6 and 2.1(260/280) and above 1.3 (260/230). cDNA libraries were prepared according to the Lexogen manual, using 500ng of total input RNA per sample and 12 cycles of PCR amplification. 64 unique, dual index barcodes were used and samples were then pooled.
QuantSeq 3’mRNA sequencing FWD (RNAseq) libraries (Lexogen) were prepared as stated in the Lexogen manual using 500ng of total input RNA per sample and 12 cycles of PCR amplification. 64 unique, dual index barcodes were used and samples were then pooled. Unique molecular identifiers were used in place of SS1.
Pooled samples were exonuclease VII treated and sequenced on the HiSeq4000 to generate Single End 100 base pair reads.

treatment_protocol: 8–10 week-old female C576B/L mice were paired with males. Insemination was confirmed by the presence of a vaginal plug the following morning, marking the gestational time as embryonic day (ED) 0.5. On embryonic day 12.5, pregnant dams were intraperitoneally administered 20mg/kg γ-irradiated Poly I:C (Sigma) to stimulate maternal immune activation. Control groups were administered saline.

tag: litter

tag: uterine horn position

value: A

tag: Sex

value: Female

tag: embryo age in days of gestation

tag: treatment on ex

value: Saline

tag: strain


title: 207760740083_R01C01

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Human cell line DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

tag: modification

value: Hela


title: Placenta_Poly IC_F_repl3

description: 3' Quant seq with UMI tags

value: F

value: Poly IC


title: 0.316uM_Sulforaphane_MCF7, M_262

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
M_262
MCF7_Sulforaphane_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC). Proliferation media consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% FBS (Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). The plating medium consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% Heat-Inactivated FBS (HI FBS; Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). For passaging, cells were washed with sterile DPBS and enzymatically removed using 0.25% trypsin-EDTA (Gibco). In preparation for the proliferation assay, A549 cells were thawed (2.0 x 106, passage 3) and placed into a T25 flask (CytoOne; USA Scientific, Ocala, FL). After 5 days in culture, cells were passaged into a T75 flask (2.0 x 106, passage 4) using a plating medium (10% HI FBS). After 5 days, cells were plated at a density of 35,000 cells/well in black-walled, clear-bottom, tissue-culture-treated 96-well plates (Greiner Bio-One) using a plating medium (10% HI FBS). Cells were cultured for 48 h in 96-well plates prior to treatment.

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads

value: tumorigenic breast epithelial cell

tag: treatment

value: MCF7 cells treated with 0.316uM Sulforaphane


title: 3.16uM_Sulforaphane_MCF7, M_264

description:
M_264
MCF7_Sulforaphane_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 3.16uM Sulforaphane


title: 207760740056_R07C01


title: Placenta_Poly IC_F_repl7

description: 3' Quant seq with UMI tags

value: D


title: 1uM_Sulforaphane_MCF7, M_263

description:
M_263
MCF7_Sulforaphane_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Sulforaphane


title: Placenta_Poly IC_M_repl5

description: 3' Quant seq with UMI tags

value: Male


title: 207760740083_R05C01


title: 0.0316uM_Sulforaphane_MCF7, M_260

description:
M_260
MCF7_Sulforaphane_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Sulforaphane


title: Brain_Saline_M_repl8

description: 3' Quant seq with UMI tags

source_name: brain


title: 207760740056_R03C01


title: Placenta_Poly IC_F_repl2

description: 3' Quant seq with UMI tags


title: Placenta_Poly IC_F_repl4

description: 3' Quant seq with UMI tags

value: C


title: 207760740056_R01C01


title: Placenta_Poly IC_F_repl1

description: 3' Quant seq with UMI tags

value: B


title: 207760740041_R07C01


title: Brain_Saline_M_repl7

description: 3' Quant seq with UMI tags


title: 0.01uM_Sulforaphane_MCF7, M_259

description:
M_259
MCF7_Sulforaphane_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM Sulforaphane


title: 207760740041_R05C01


title: Brain_Saline_M_repl5

description: 3' Quant seq with UMI tags


title: Brain_Saline_M_repl6

description: 3' Quant seq with UMI tags


title: 0.00316uM_Sulforaphane_MCF7, M_258

description:
M_258
MCF7_Sulforaphane_0.00316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.00316uM Sulforaphane


title: Brain_Saline_M_repl3

description: 3' Quant seq with UMI tags


title: 0.001uM_Sulforaphane_MCF7, M_257

description:
M_257
MCF7_Sulforaphane_0.001uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.001uM Sulforaphane


title: Brain_Saline_M_repl2

description: 3' Quant seq with UMI tags


title: ΔaslB rep 3

city: Utrecht

first: Peter Jan

last: Vonk

state: Utrecht

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

description: P2: 100 cycles. 2x50bp

data_processing:
Reads were trimmed with bbduk, part of the bbmap suite. Version 38.99. Minimum base quality 20, minimum read length 20
Alignment with hisat2 version 2.2.1. Minimum intronlength 20, maximum intronlength 1000
Differential expression was called with cuffdiff for all conditions
Read counts were obtained with subRead featureCounts
Assembly: Aspergillus Fumigatus N402 reference assembly
Supplementary files format and content: tab delimited matrix of the total counts for each transcript (one transcript per gene). Columns are each biological replicate per sample.
Supplementary files format and content: Excel file with the FPKM for each condition, the differential expression analysis between each condition and the qValue/significance of each comparison as determined by cuffdiff. Functional annotations are included and were obtained from the AspniN402 database hosted at the JGI mycocosm website

organism: Aspergillus niger

source_name: knockout strain

growth_protocol: Total RNA of A. niger was isolated from 16 h TM-G( MM with 0.5% yeast extract and 0.2% casamino acids with 25 mM glucose as a carbon source) and 4 h MM-X(MM with 25 mM xylose) liquid shaking cultures.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, www.thermofisher.com). The RNA was purified using the Rnase Plant Mini Kit (Qiagen) and quantified with a Nanodrop ND-1000 (Thermo Scientific, www.thermofisher.com).
Libraries were prepared with the Trueseq RNA stranded polyA kit according to manufacturer's specification

treatment_protocol: Mycelium of biological triplicates of liquid shaken cultures of A. niger strains MA234.1, ΔaslA, and ΔaslB were homogenized in a Tissue Lyzer II (Qiagen) under liquid nitrogen.

value: vegetative mycelium

tag: strain background

tag: genotype

value: {delta}aslB

value: Grown on liquid shaking culture


title: 0.1uM_Sulforaphane_MCF7, M_261

description:
M_261
MCF7_Sulforaphane_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Sulforaphane


title: 0uM_Sulforaphane_MCF7, M_256

description:
M_256
MCF7_Sulforaphane_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM Sulforaphane


title: 207760740041_R03C01

value: Hela


title: Brain_Saline_F_repl8

description: 3' Quant seq with UMI tags

value: Female

value: Saline


title: ΔaslB rep 1

description: P2: 100 cycles. 2x50bp


title: ΔaslB rep 2

description: P2: 100 cycles. 2x50bp


title: 0.0316uM_Sulforaphane_MCF7, M_255

description:
M_255
MCF7_Sulforaphane_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell


title: 207760740030_R05C01


title: 0.01uM_Sulforaphane_MCF7, M_254

description:
M_254
MCF7_Sulforaphane_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Brain_Saline_F_repl7

description: 3' Quant seq with UMI tags

value: F


title: ΔaslA rep 3

description: P2: 100 cycles. 2x50bp

value: {delta}aslA


title: Brain_Saline_F_repl6

description: 3' Quant seq with UMI tags

value: D


title: 207760740030_R01C01


title: ΔaslA rep 2

description: P2: 100 cycles. 2x50bp


title: Brain_Saline_M_repl4

description: 3' Quant seq with UMI tags

value: Male


title: Brain_Saline_F_repl5

description: 3' Quant seq with UMI tags


title: ΔaslA rep 1

description: P2: 100 cycles. 2x50bp


title: 0uM_Sulforaphane_MCF7, M_251

description:
M_251
MCF7_Sulforaphane_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207760740041_R01C01


title: Brain_Saline_F_repl4

description: 3' Quant seq with UMI tags


title: M234-1 rep 3

description: P2: 100 cycles. 2x50bp


title: 0.0316uM_Sulforaphane_MCF7, M_250

description:
M_250
MCF7_Sulforaphane_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Sulforaphane


title: 207760740030_R07C01


title: Brain_Saline_F_repl3

description: 3' Quant seq with UMI tags

value: E


title: M234-1 rep 2

description: P2: 100 cycles. 2x50bp


title: Brain_Saline_F_repl2

description: 3' Quant seq with UMI tags


title: 207675480016_R07C03

value: 50% Epigen Control


title: 207675480016_R05C03


title: M234-1 rep 1

description: P2: 100 cycles. 2x50bp


title: 207675480016_R06C02


title: Brain_Poly IC_M_repl8

description: 3' Quant seq with UMI tags

value: Poly IC


title: 0.00316uM_Sulforaphane_MCF7, M_253

description:
M_253
MCF7_Sulforaphane_0.00316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.00316uM Sulforaphane


title: Brain_Saline_F_repl1

description: 3' Quant seq with UMI tags

value: A


title: 207760740030_R03C01


title: eWAT, epinephrine injected, biol rep 6

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

institute: McMaster University

data_processing:
Raw sequencing files imported into Galaxy (usegalaxy.org) for quality control and processing steps
FastQC tool used to check read quality
Cutadapt tool used to trim adaptor sequences and low quality reads
Remaining reads were mapped to mm10 reference genome with the HISAT2 tool
Counts were quantified with the featureCounts tool and imported into R for gene expression analyses
Counts data were VST-normalized in R using the DESeq2 package
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample

source_name: eWAT

extract_protocol:
Tissues were homogenized in TRIzol reagent. An RNeasy kit (Qiagen, Cat# 74106) was used for subsequent total RNA extraction and purification according manufacturers instruction.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Epinephrine condition: Sodium epinephrine (Sigma-Aldrich, E4642) was diluted in saline and injected intraperitoneal (IP; ~0900) at a dosage of 0.5 mg/kg body weight. eWAT was collected after 1h.
Vehicle condition: Saline injected intraperitoneal (IP; ~0900) at the same volume as epinephrine. eWAT was collected after 1h.

value: eWAT

tag: mouse line

tag: agent

value: sodium epinephrine (Sigma-Aldrich, E4642)

tag: diet

value: chow

tag: age

value: 23 weeks


title: 207675480016_R12C02

tag: tissue

value: 100% Epigen Control


title: 0.00316uM_Sulforaphane_MCF7, M_248

description:
M_248
MCF7_Sulforaphane_0.00316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

tag: cell line


title: 207675480016_R11C03


title: eWAT, epinephrine injected, biol rep 5

value: 22 weeks


title: 0.001uM_Sulforaphane_MCF7, M_252

description:
M_252
MCF7_Sulforaphane_0.001uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

tag: cell type

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 0.001uM Sulforaphane


title: 0.001uM_Sulforaphane_MCF7, M_247

description:
M_247
MCF7_Sulforaphane_0.001uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480016_R08C02


title: Brain_Poly IC_M_repl7

description: 3' Quant seq with UMI tags

tag: litter


title: Brain_Saline_M_repl1

description: 3' Quant seq with UMI tags

tag: uterine horn position

value: Saline


title: Brain_Poly IC_M_repl6

description: 3' Quant seq with UMI tags

value: F

tag: Sex


title: 207675480016_R10C02


title: eWAT, epinephrine injected, biol rep 3

value: Male

value: 20 weeks


title: 0.01uM_Sulforaphane_MCF7, M_244

description:
M_244
MCF7_Sulforaphane_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM Sulforaphane


title: 0.01uM_Sulforaphane_MCF7, M_249

description:
M_249
MCF7_Sulforaphane_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480016_R09C03


title: 0.0316uM_Sulforaphane_MCF7, M_245

description:
M_245
MCF7_Sulforaphane_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Sulforaphane


title: 207675480016_R04C02

value: 0% Epigen Control


title: 0.001uM_Sulforaphane_MCF7, M_242

description:
M_242
MCF7_Sulforaphane_0.001uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: eWAT, epinephrine injected, biol rep 2

value: 19 weeks


title: Brain_Poly IC_M_repl5

description: 3' Quant seq with UMI tags

value: D

tag: embryo age in days of gestation

value: Poly IC


title: Brain_Poly IC_M_repl3

description: 3' Quant seq with UMI tags

value: C

tag: treatment on ex


title: eWAT, epinephrine injected, biol rep 1

value: eWAT

value: sodium epinephrine (Sigma-Aldrich, E4642)

value: chow

value: 18 weeks


title: Brain_Poly IC_M_repl4

description: 3' Quant seq with UMI tags

tag: strain


title: 207675480016_R03C03

tag: modification


title: 0uM_Sulforaphane_MCF7, M_246

description:
M_246
MCF7_Sulforaphane_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

tag: treatment

value: MCF7 cells treated with 0uM Sulforaphane


title: 207675480016_R01C03


title: 0.00316uM_Sulforaphane_MCF7, M_243

description:
M_243
MCF7_Sulforaphane_0.00316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.00316uM Sulforaphane


title: eWAT, saline injected, biol rep 6

value: saline

value: 17 weeks


title: Brain_Poly IC_M_repl2

description: 3' Quant seq with UMI tags

value: Male


title: 100uM_Paraquat_MCF7, M_240

description:
M_240
MCF7_Paraquat_100uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 100uM Paraquat


title: eWAT, saline injected, biol rep 4

value: 15 weeks


title: eWAT, epinephrine injected, biol rep 4

value: 21 weeks


title: 0uM_Sulforaphane_MCF7, M_241

description:
M_241
MCF7_Sulforaphane_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R16C02


title: 207675480016_R02C02

value: 0% Epigen Control


title: Brain_Poly IC_M_repl1

description: 3' Quant seq with UMI tags

value: F


title: eWAT, saline injected, biol rep 3

value: 14 weeks


title: 31.6uM_Paraquat_MCF7, M_239

description:
M_239
MCF7_Paraquat_31.6uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 31.6uM Paraquat


title: Brain_Poly IC_F_repl7

description: 3' Quant seq with UMI tags

value: D

value: Female

value: Poly IC


title: 10uM_Paraquat_MCF7, M_238

description:
M_238
MCF7_Paraquat_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Paraquat


title: eWAT, saline injected, biol rep 5

value: eWAT

value: chow

value: 16 weeks


title: eWAT, saline injected, biol rep 2

value: saline

value: 13 weeks


title: Brain_Poly IC_F_repl8

description: 3' Quant seq with UMI tags


title: 207675480011_R14C02


title: 207675480011_R12C02


title: Brain_Poly IC_F_repl6

description: 3' Quant seq with UMI tags


title: eWAT, saline injected, biol rep 1

value: Male

value: 12 weeks


title: Brain_Poly IC_F_repl5

description: 3' Quant seq with UMI tags


title: 1uM_Paraquat_MCF7, M_236

description:
M_236
MCF7_Paraquat_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 1uM Paraquat


title: 207675480011_R10C02


title: te2_2

city: Norfolk

first: Petra

last: Popovics

state: Virginia

address: 651 Colley Avenue Room 422

institute: Eastern Virginia Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to Mus musculus GRCm39 (Ensembl release 111) cDNA reference for all annotated RNA was prepared using kallisto (v0.46.1) and bustools (v0.39.4). Transcript counts were aggregated to gene counts using bustools. The count matrix was imported into R (v4.3.2, Bioconductor v3.18.1) and analyzed using Seurat package (v. 5.0.1) and was filtered such that each cell had a minimum of 200 genes and those genes were detected in at least 3 cells.
Assembly: mus musculus GRCm39 (Ensembl release 111)
Supplementary files format and content: tab-separated values files

source_name: ventral prostate

extract_protocol:
Paired ventral prostate lobes were collected into one tube for each animal in ice-cold PBS and were transferred to 100 ul of 10 mg/mL (in HBSS) Bacillus licheniformis protease (Creative Enzymes, Shirley, NY). Tissues were agitated at 6°C at speeds ranging from 600 to 1000 rpm for up to one hour, with intermittent pipetting, until noticeable cell separation was observed. Cells were then passed through a 40µm mesh strainer and cell viability was assessed on a Countess 3 FL and ranged between 72-78 %. Following the guidelines from the Chromium Next GEM Single Cell manual, we determined the optimal cell loading to be 7000 cells per sample.
Cells were barcoded and libraries were generated for duplicate samples per group using the Chromium Next GEM Single Cell 3ʹ Kit v3.1. Libraries were created from each animal and concentrations were calculated based on Tapestation data (200-1000 bp). Paired-end sequencing was conducted on a NextSeq2000 instrument.

value: ventral prostate

value: various

value: wt


title: Brain_Poly IC_F_repl4

description: 3' Quant seq with UMI tags

value: C


title: 100uM_Paraquat_MCF7, M_235

description:
M_235
MCF7_Paraquat_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 100uM Paraquat


title: 207675480011_R08C02


title: Brain_Poly IC_F_repl3

description: 3' Quant seq with UMI tags

value: F

value: Female


title: sham2

description: 10x Genomics

value: sham


title: 31.6uM_Paraquat_MCF7, M_234

description:
M_234
MCF7_Paraquat_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 31.6uM Paraquat


title: 207675480011_R04C02


title: sham1

description: 10x Genomics


title: Brain_Poly IC_F_repl2

description: 3' Quant seq with UMI tags

value: Poly IC


title: 207675480011_R02C02


title: Brain_Poly IC_F_repl1

description: 3' Quant seq with UMI tags

value: B


title: 3.16uM_Paraquat_MCF7, M_232

description:
M_232
MCF7_Paraquat_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 3.16uM Paraquat


title: Single cell cultured control SMG (no dispase)

city: Bethesda

first: Rei

last: Sekiguchi

state: Maryland

address: 30 Convent Drive

department: CBS

institute: NIDCR

data_processing:
Reads were mapped using GRCm38-2020-A reference transcriptome
Sequencing data was processed using the 10X genomics Cell Ranger v6.1.1 pipeline
Secondary analysis was performed using Seurat v4 R package
Secondary analysis was performed using NichenetR R package
Assembly: Reads were mapped using GRCm38-2020-A reference transcriptome (10X Genomics)
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Submandibular gland

extract_protocol:
Accutase and Accumax
Single-cell RNA capture was performed using a 10X Genomics Chromium Controller instrument. Libraries were generated following the 10X Genomics 3’ Gene Expression  v3

value: Submandibular gland

value: Wid type

value: control


title: 1uM_Paraquat_MCF7, M_231

description:
M_231
MCF7_Paraquat_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell


title: 207675480011_R15C03


title: RNA-seq_WT mice, C. mast inoculated, rep3

first: Vijay

last: Nagarajan

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

description:
sample name:
Vg6_treat_WT3

data_processing:
Pre-processing, Cudadapt
Alignment, annotation, STAR
Quantification and analysis, STAR, RSEM
Differential expression analysis, Partek
Assembly: mm10
Supplementary files format and content: .txt, tab delimited text matrix file, RAW counts generated by RSEM

extract_protocol:
Singe cell suspensions were prepared from cervical lymph nodes and spleen of WT or TLR2-/- mice. DAPI-CD90.2+TCRβ-TCRγδ+Vγ1-Vγ4-CD27-CD44hi cells were sorted from naïve WT, naïve TLR2-/-, C. mast inoculated WT, and C. mast inoculated TLR2-/- mice. RNA was isolated using Qiagen miRNeasy Micro Kit. RNA was run on Agilent 2100 Bioanalyzer and RIN >8.0 was aimed to pass QC.
RNA-seq was performed on Illumina Hiseq4000 (150pb, paired) using Clontech RNA Ultra Low Input Library Prep and paired-end sequencing in the NCI sequencing facility

value: WT

value: C. mast


title: 3.16uM_Paraquat_MCF7, M_237

description:
M_237
MCF7_Paraquat_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq_WT mice, C. mast inoculated, rep2

description:
sample name:
Vg6_treat_WT2


title: 207675480011_R13C03


title: Single cell cultured SMG-epithelium + PG mesenchyme

value: recombination


title: 100uM_Paraquat_MCF7, M_230

description:
M_230
MCF7_Paraquat_100uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Single cell cultured control SMG (dispase treated)


title: 207675480011_R11C03


title: 31.6uM_Paraquat_MCF7, M_229

description:
M_229
MCF7_Paraquat_31.6uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq_TLR2-deficient mice, C. mast inoculated, rep3

description:
sample name:
Vg6_treat_KO3


title: 207675480011_R06C02


title: RNA-seq_WT mice, C. mast inoculated, rep1

description:
sample name:
Vg6_treat_WT1


title: 207675480011_R09C03


title: Single cell cultured control PG (dispase treated)

source_name: Parotid gland

value: Parotid gland


title: te2_1

description: 10x Genomics

value: ventral prostate

value: various

value: wt


title: 10uM_Paraquat_MCF7, M_233

description:
M_233
MCF7_Paraquat_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 10uM Paraquat


title: 3.16uM_Paraquat_MCF7, M_227

description:
M_227
MCF7_Paraquat_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 10uM_Paraquat_MCF7, M_228

description:
M_228
MCF7_Paraquat_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R05C03


title: Single cell cultured control PG (no dispase)


title: RNA-seq_TLR2-deficient mice, C. mast inoculated, rep2

description:
sample name:
Vg6_treat_KO2


title: Single cell cultured PG-epithelium + SMG mesenchyme


title: 207675480011_R03C03


title: RNA-seq_TLR2-deficient mice, C. mast inoculated, rep1

description:
sample name:
Vg6_treat_KO1


title: 1uM_Paraquat_MCF7, M_226

description:
M_226
MCF7_Paraquat_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 1uM Paraquat


title: RNA-seq_WT mice, naïve, rep3

description:
sample name:
Vg6_naive_WT3

value: naive


title: 100uM_Paraquat_MCF7, M_225

description:
M_225
MCF7_Paraquat_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 100uM Paraquat


title: 207675480011_R01C03


title: RNA-seq_WT mice, naïve, rep2

description:
sample name:
Vg6_naive_WT2


title: 31.6uM_Paraquat_MCF7, M_224

description:
M_224
MCF7_Paraquat_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 31.6uM Paraquat


title: 207675480011_R15C02


title: 10uM_Paraquat_MCF7, M_223

description:
M_223
MCF7_Paraquat_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq_WT mice, naïve, rep1

description:
sample name:
Vg6_naive_WT1


title: 4 hours, IL-12 block, IFNg block, mouse 3

city: Pittsburgh

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: C57BL/6 purified B cells cultured 4 hours

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.5).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.3) (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.0c) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: Spleen

extract_protocol:
Cells were washed in PBS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C. RNA purification was performed using the Qiagen RNeasy Micro Plus Kit.
cDNA was generated using the Takara Smart-Seq v4 Ultra Low Input RNA kit. Libraries were prepared using Illumina Nextera FLEX Kit with UDI set B indexes. Samples were sequenced using NextSeq 2000 P3 reagents (200 cycles) to obtain 20M 2x101 bp reads.

treatment_protocol: Cells were stimulated for 4 or 24 hours with LPS and the indicated cytokines or blocking antibodies.

value: Spleen

value: 4 hours, IL-12 block, IFNg block


title: RNA-seq_TLR2-deficient mice, naïve, rep2

description:
sample name:
Vg6_naive_KO3


title: 3.16uM_Paraquat_MCF7, M_222

description:
M_222
MCF7_Paraquat_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 3.16uM Paraquat


title: 207675480011_R07C03


title: 4 hours, IL-12 block, IFNg block, mouse 2


title: RNA-seq_TLR2-deficient mice, naïve, rep1

description:
sample name:
Vg6_naive_KO2


title: 207675480011_R11C02


title: 207675480011_R13C02


title: 4 hours, IL-12 block, IFNg block, mouse 1


title: 1uM_Paraquat_MCF7, M_221

description:
M_221
MCF7_Paraquat_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 4 hours, no added IL-12 nor blocked, IFNg at 3 ng/mL, mouse 3


title: 4 hours, IL-12 block, IFNg at 3 ng/mL, mouse 3

value: 4 hours, IL-12 block, IFNg at 3 ng/mL


title: 0.316uM_Paraquat_MCF7, M_220

description:
M_220
MCF7_Paraquat_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 0.316uM Paraquat


title: WT mice, PBS treated, rep2

library_source: genomic

data_processing:
Data quality, FastQC, 0.11.9
Pre-processing, FastP, 0.20.1
Alignment, Bowtie 2, 2.4.1
Peak calling, Genrich, 0.6
Differential expression analysis, DESeq2, 1.30.1
Assembly: mm10
Supplementary files format and content: .narrowPeak, text file, peaks called with Genrich

extract_protocol:
Singe cell suspensions were prepared from cervical lymph nodes and spleen of WT or TLR2-/- mice. DAPI-CD90.2+TCRβ-TCRγδ+Vγ1-Vγ4-CD27-CD44hi cells were sorted from naïve WT, naïve TLR2-/-, C. mast inoculated WT, and C. mast inoculated TLR2-/- mice. The nuclei extracted from the cells were used for library preparation.
The nuclei extracted from the cells were quality controlled and suspended in the TruePrep Tagment Enzyme mix and incubated at 37°C for 30 min, followed by PCR amplification and purification with the AMPure beads. The quality-controlled library was quantified with Qubit 2.0, clustered using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) and sequenced on an Illumina Hiseq platform, to generate 150 bp paired-end reads.

value: WT

value: PBS


title: 207675480011_R07C02


title: 4 hours, IL-12 block, IFNg at 3 ng/mL, mouse 2


title: WT mice, PBS treated, rep1


title: 207675480011_R05C02


title: 0.1uM_Paraquat_MCF7, M_219

description:
M_219
MCF7_Paraquat_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Paraquat


title: 4 hours, no added IL-12 nor blocked, IFNg at 3 ng/mL, mouse 1


title: 0.0316uM_Paraquat_MCF7, M_218

description:
M_218
MCF7_Paraquat_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Paraquat


title: WT mice, C. mast inoculated, rep1

value: C. mast


title: 4 hours, no added IL-12 nor blocked, IFNg at 3 ng/mL, mouse 2


title: 207675480011_R01C02


title: 4 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 3

value: 4 hours, IL-12 block, IFNg at 0.5 ng/mL


title: 207675480011_R03C02


title: 0.01uM_Paraquat_MCF7, M_217

description:
M_217
MCF7_Paraquat_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM Paraquat


title: 0uM_Paraquat_MCF7, M_216

description:
M_216
MCF7_Paraquat_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM Paraquat


title: TLR2-deficient mice, PBS treated, rep1


title: 207675480011_R16C01


title: 207675480011_R09C02


title: 0.316uM_Paraquat_MCF7, M_215

description:
M_215
MCF7_Paraquat_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: TLR2-deficient mice, PBS treated, rep2


title: 207675480011_R16C03


title: 4 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 2


title: TLR2-deficient mice, C. mast inoculated, rep2


title: 207675480011_R14C01


title: 207675480011_R12C01


title: TLR2-deficient mice, C. mast inoculated, rep1


title: 0.1uM_Paraquat_MCF7, M_214

description:
M_214
MCF7_Paraquat_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.0316uM_Paraquat_MCF7, M_213

description:
M_213
MCF7_Paraquat_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: WT mice, C. mast inoculated, rep2


title: 24 hours, IL-12 block, IFNg block, mouse 2

description: C57BL/6 purified B cells cultured 24 hours

value: 24 hours, IL-12 block, IFNg block


title: 4 hours, IL-12 block, IFNg at 3 ng/mL, mouse 1


title: 24 hours, IL-12 block, IFNg block, mouse 3


title: 207675480011_R10C01


title: 0.01uM_Paraquat_MCF7, M_212

description:
M_212
MCF7_Paraquat_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 24 hours, IL-12 block, IFNg block, mouse 1


title: AThi oHSC_3

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

data_processing:
Sequencing QC was performed using FastQC and MultiQC. Ingenuity pathway analysis was used in genes passing a log 2-fold change greater than or equal to 1 or less than or equal to -1 and FDR <0.05 cutoff.
Paired-end reads were mapped to the mouse reference genome (GRCm38 ver104) using STAR and quantified with FeatureCounts. Gene counts were imported into a DDS object using DESeq2  removing genes with less than 100 reads summed across all included samples.
The rlog transformation implemented in DESeq2 was utilized to normalize sample read counts for exploratory data analysis, including principal component analysis (PCA) and hierarchical clustering. For yHSC, AThi oHSC, and ATlo oHSC RNA-seq samples, we created a linear model regressing out the “sort day” batch effect, design(dds) = formula (~sortBatch + group). The Benjamini-Hochberg algorithm was used for multiple testing correction, with an FDR = 0.05 significance threshold.
Gene Set Enrichment Analysis (GSEA) was performed for indicated pairwise comparisons using gene symbol log2 fold change pre-ranked files using the classic enrichment statistic, gene sets with a minimum size of 15 and maximum size of 500 genes, the mouse gene symbol remapping MSigDB.v7.0 chip, and the c2.cp.recatome.v6.2.symbols curated gene database.
Ingenuity pathway analysis was used in genes passing a log 2-fold change greater than or equal to 1 or less than or equal to -1 and FDR <0.05 cutoff.
Assembly: GRCm38 ver104
Supplementary files format and content: CSV of differentially expressed genes for each pairwise comparison
Supplementary files format and content: CSV of upstream regulators detected by IPA analysis for AThi oHSC vs ATlo oHSC significantly DE genes.

source_name: bone marrow

extract_protocol:
RNA was isolated from ~10,000 HSCs using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA integrity number (RIN) was determined by Bioanalyzer (Agilent Technologies) and RNA samples with RIN > 9.0 were further processed. RNA samples were processed over two experimental “sort days” and stored at -80°C in RNA isolation buffer until library preparation. A total of 3 paired AThi/ATlo oHSC biological replicates were sequenced alongside 2 yHSC replicates. RNA was quantified and QC using an Agilent Bioanalyzer. Illumina sequencing libraries were prepared and sequenced at the NYU Genome Technology Center (New York, NY).
The NuGen Ovation Trio low input RNA-seq library preparation kit was used for library preparation.
All libraries were prepared at the same time in order to minimize batch effects. Libraries were sequenced using an Illumina HiSEQ 4000 instrument with paired end 50 base pair sequencing to a target depth of 40 million unique reads per sample.

value: bone marrow

value: purified hematopoietic stem cell

value: Old

tag: autophagy status

value: AThi (GFPlo)

value: steady state isolation


title: 207675480011_R08C01


title: 24 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 3

value: Spleen


title: ATlo oHSC_2

value: ATlo (GFPhi)

tag: genotype


title: 24 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 2


title: 4 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 1


title: 0.316uM_Paraquat_MCF7, M_210

description:
M_210
MCF7_Paraquat_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: MCF7 cells treated with 0.316uM Paraquat


title: AThi oHSC_2


title: 207675480011_R04C01


title: 24 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 1


title: ATlo oHSC_3


title: 0.0316uM_Paraquat_MCF7, M_208

description:
M_208
MCF7_Paraquat_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R02C01


title: ATlo oHSC_1


title: 24 hours, IL-12 at 20 pg/mL, IFNg block, mouse 3

value: 24 hours, IL-12 at 20 pg/mL, IFNg block


title: AThi oHSC_1


title: 207675480011_R08C03


title: 0.01uM_Paraquat_MCF7, M_207

description:
M_207
MCF7_Paraquat_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0uM_Paraquat_MCF7, M_206

description:
M_206
MCF7_Paraquat_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 24 hours, IL-12 at 20 pg/mL, IFNg block, mouse 2


title: yHSC_1

value: Young

value: unfractionated


title: 0uM_Paraquat_MCF7, M_211

description:
M_211
MCF7_Paraquat_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.316uM_Paraquat_MCF7, M_205

description:
M_205
MCF7_Paraquat_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R16C02


title: 207675480004_R14C02


title: 24 hours, IL-12 at 20 pg/mL, IFNg block, mouse 1


title: O3 ATlo

data_processing:
Nextera sequencing adapter contamination  was removed using the Trim Galore Cutadapt wrapper in paired end mode
BWA was used to align samples to the GRCm38 ver 104 genome. BAM files were quality controlled by looking at the distribution of reads aligning to chromosomes and the distribution of insert sizes.
Peaks were called using MACS2, removing PCR duplicates. NarrowPeak files generated by MACS2 were quality controlled for distribution of reads mapping to GRCm38 genomic regions using the R CHIPseeker package and Tx.Db.mmusculus.UCSC.mm39.refGene annotation.
For differential ATAC-seq, a GRanges consensus peak object was generated using ChIPQC containing non-redundant open regions present in any sample. Nucleosome free regions (<100bp fragment length) from sample BAM files were counted using FeatureCounts against the consensus peak annotation. Sample counts were imported into a dds object using DESeq2, and exploratory data analysis was performed using rlog normalized count data and PCA. For differential peak accessibility calling between groups, we used DESeq2 using the results function and the DESeq2 estimator.
For pathway enrichment analysis, we annotated promoter proximal peaks within ± 1000bp of the transcription start site (TSS) using TxDb.Mmusculus.UCSC.mm39.refGene. For AThi oHSC, ATlo oHSC, and yHSC samples, we used GSEA analysis using the GSEA software and MSigDB Hallmark pathways.
Assembly: GRCm38 ver 104 genome
Supplementary files format and content: BAM files for each sample
Supplementary files format and content: BigWig files for each sample
Supplementary files format and content: Macs2 narrowpeak files for each sample
Supplementary files format and content: csv files containing differentially accessible peaks for each pairwise comparison

extract_protocol:
HSCs were sorted into 400 µl staining media, washed with 1 ml PBS and spun down at 500 g for 5 min at 4°C. Liquid was carefully aspirated and pellets were resuspended in 50 µl ATAC-seq lysis buffer (ATAC-RSB [1M Tris-HC1 pH 7.4, 5M NaCl, and 1M MgCl2 in water] with 0.1% Tween 20, 0.01% digitonin and 0.1% NP40) and left on ice for 3 min. Samples were then washed with 1 ml ATAC Wash buffer (ATAC-RSB with 0.1% Tween 20), inverted to mix, spun for 10 min at 500 g at 4°C, and resuspended in 20 µl ATAC transposition buffer (Nextera TD Buffer (Illumina) with 100 nM Nextera Transposase (Illumina), 0.01% Digitonin and 0.01% Tween 20 in PBS). DNA was transposed for 30 min at 37°C, purified using the ZYMO clean and concentrator-5 kit (Zymo), eluted in 22 µl Zymo Elution buffer, then stored at -20°C until library preparation.
Libraries were pre-amplified with a common Ad1 adapter and unique Ad2 adapter sequences, and additionally amplified using qPCR cycle determination with the NEBNext® High-Fidelity 2X PCR Master Mix (NEB). All libraries were prepared on the same day to limit library preparation-associated batch effects. Double sided AMPure XP bead purification kit (Beckman Coulter) was utilized to remove primer-dimers and large fragments > 1000bp. Libraries were QC using Qubit and Agilent Bioanalyzer at the CUMC Herbert Irving Comprehensive Cancer Center Molecular Pathology core.
Samples were sequenced by GENEWIZ using paired end 150bp sequencing on a HiSeq400 instrument to a target depth of 100 million unique reads per sample. Sequencing quality control was performed using FastQC and MultiQC

value: hematopoietic stem cell

value: ATlo( GFPhi)


title: yHSC_2


title: 24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 3


title: 207675480011_R06C01


title: 24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 2


title: 0.1uM_Paraquat_MCF7, M_204

description:
M_204
MCF7_Paraquat_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.1uM Paraquat


title: 0.1uM_Paraquat_MCF7, M_209

description:
M_209
MCF7_Paraquat_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R12C02


title: 24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 1


title: O3 AThi


title: 207675480004_R10C02


title: 0.0316uM_Paraquat_MCF7, M_203

description:
M_203
MCF7_Paraquat_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.0316uM Paraquat


title: 0.01uM_Paraquat_MCF7, M_202

description:
M_202
MCF7_Paraquat_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0.01uM Paraquat


title: O2 ATlo

value: bone marrow


title: 207675480004_R08C02


title: 4 hours, IL-12 at 20 pg/mL, IFNg block, mouse 3

description: C57BL/6 purified B cells cultured 4 hours

value: 4 hours, IL-12 at 20 pg/mL, IFNg block


title: 0uM_Paraquat_MCF7, M_201

description:
M_201
MCF7_Paraquat_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: MCF7 cells treated with 0uM Paraquat


title: O2 AThi

value: purified hematopoietic stem cell

value: AThi (GFPlo)


title: 100uM_Prochloraz_A549, A_400

description:
A_400
A549_Prochloraz_100uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 100uM Prochloraz


title: 207675480004_R04C02


title: 4 hours, IL-12 at 20 pg/mL, IFNg block, mouse 2

value: Spleen


title: O1 ATlo

value: steady state isolation


title: 4 hours, IL-12 at 20 pg/mL, IFNg block, mouse 1


title: 31.6uM_Prochloraz_A549, A_399

description:
A_399
A549_Prochloraz_31.6uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: A549 cells treated with 31.6uM Prochloraz


title: Young_5

value: Unfractionated


title: 10uM_Prochloraz_A549, A_398

description:
A_398
A549_Prochloraz_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Prochloraz


title: 207675480004_R02C02


title: 207675480011_R12C03


title: O1 AThi

value: hematopoietic stem cell


title: 4 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 2


title: 4 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 3


title: 3.16uM_Prochloraz_A549, A_397

description:
A_397
A549_Prochloraz_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Prochloraz


title: Young_4


title: 207675480004_R16C03


title: 4 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 1


title: 1uM_Prochloraz_A549, A_396

description:
A_396
A549_Prochloraz_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Prochloraz


title: Young_3


title: 207675480004_R14C03


title: Young_2


title: 4 hours, IL-12 at 200 pg/mL, IFNg block, mouse 3

value: 4 hours, IL-12 at 200 pg/mL, IFNg block


title: 4 hours, IL-12 at 200 pg/mL, IFNg block, mouse 2


title: 207675480004_R06C02


title: 100uM_Prochloraz_A549, A_395

description:
A_395
A549_Prochloraz_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R12C03


title: Young_1


title: O5_Tail

data_processing:
Bowtie2 was used to align Fastq files to mouse genome.
Somatic mutations relative to tail control were called with MuTect2.

source_name: tail

extract_protocol:
Cell pellets containing ~ 10,000 HSCs per sample were frozen dry and sent to the Memorial Sloan Kettering Cancer Center Sequencing Core Facility (New York, NY) or to Genewiz (South Plainfield, NJ).
DNA was prepared for whole exome capture and sequencing by these services.
AThi and ATlo oHSC DNA samples were sequenced to 150X coverage and tail control DNA from each biological replicate was sequenced to 30X depth with paired end sequencing.

value: tail

value: tail tissue

value: Old


title: 31.6uM_Prochloraz_A549, A_394

description:
A_394
A549_Prochloraz_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 10uM_Prochloraz_A549, A_393

description:
A_393
A549_Prochloraz_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 4 hours, IL-12 at 200 pg/mL, IFNg at 0.5 ng/mL, mouse 3


title: 207675480004_R10C03


title: 4 hours, IL-12 at 200 pg/mL, IFNg block, mouse 1


title: 207675480004_R08C03


title: 207675480004_R06C03


title: O5_ATlo

value: bone marrow

value: ATlo (GFPhi)


title: 4 hours, IL-12 at 200 pg/mL, IFNg at 0.5 ng/mL, mouse 2


title: O5_AThi

value: purified hematopoietic stem cell

value: AThi (GFPlo)


title: 1uM_Prochloraz_A549, A_391

description:
A_391
A549_Prochloraz_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R04C03


title: 3.16uM_Prochloraz_A549, A_392

description:
A_392
A549_Prochloraz_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 4 hours, IL-12 at 200 pg/mL, IFNg at 0.5 ng/mL, mouse 1

value: Spleen


title: 100uM_Prochloraz_A549, A_390

description:
A_390
A549_Prochloraz_100uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 100uM Prochloraz


title: O4_Tail

value: steady state isolation


title: 4 hours, IL-12 at 2000 pg/mL, IFNg at 0.5 ng/mL, mouse 3


title: 207675480011_R10C03

value: Raji


title: 4 hours, IL-12 at 2000 pg/mL, IFNg at 0.5 ng/mL, mouse 2


title: O4_ATlo


title: 10uM_Prochloraz_A549, A_388

description:
A_388
A549_Prochloraz_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell


title: O4_AThi


title: O3_Tail


title: 207675480004_R15C03


title: 4 hours, IL-12 at 2000 pg/mL, IFNg block, mouse 3


title: 3.16uM_Prochloraz_A549, A_387

description:
A_387
A549_Prochloraz_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R13C03


title: 4 hours, IL-12 at 2000 pg/mL, IFNg at 0.5 ng/mL, mouse 1


title: O3_ATlo


title: 4 hours, IL-12 at 2000 pg/mL, IFNg block, mouse 2


title: O3_AThi


title: 1uM_Prochloraz_A549, A_386

description:
A_386
A549_Prochloraz_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 100uM_Prochloraz_A549, A_385

description:
A_385
A549_Prochloraz_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R09C03


title: 207675480004_R11C03


title: 31.6uM_Prochloraz_A549, A_384

description:
A_384
A549_Prochloraz_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Prochloraz


title: 4 hours, IL-12 at 2000 pg/mL, IFNg block, mouse 1

description: C57BL/6 purified B cells cultured 4 hours


title: O2_Tail


title: 207675480004_R02C03


title: hsp-iso2  biol rep2 7dpf

city: Shanghai

first: Jianhua

last: Guo

address: NO.2005,Songhu Road,jiangwan campus

country: China

institute: Fudan university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 whole genome using Hisat2 v2.0.5
Assembly: GRCz11
Supplementary files format and content: txt files include FPKM for each sample

organism: Danio rerio

source_name: whole larvae

growth_protocol: zebrafish were raised and maintained under standard conditions

extract_protocol:
Whole larval total RNA samples were harvested using Trizol reagent
Poly (A) RNA from 1 mg total RNA  was used to generate the cDNA libraries, according to NEBNext Ultra RNA Library Prep Kit for Illumina.

value: whole larvae

value: mbd5 overexpression

value: 38C 1hour heatshock


title: 31.6uM_Prochloraz_A549, A_389

description:
A_389
A549_Prochloraz_31.6uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: hsp-iso2 biol rep1 7dpf


title: 10uM_Prochloraz_A549, A_383

description:
A_383
A549_Prochloraz_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Prochloraz


title: 207675480004_R05C03


title: O2_AThi


title: O2_ATlo


title: 3.16uM_Prochloraz_A549, A_382

description:
A_382
A549_Prochloraz_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Prochloraz


title: O1_Tail

value: tail

value: tail tissue


title: 207675480004_R03C03


title: 1uM_Prochloraz_A549, A_381

description:
A_381
A549_Prochloraz_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Prochloraz


title: hsp-ctrl biol rep1 7dpf

value: AB WT


title: 207675480004_R01C03


title: hsp-ctrl biol rep2 7dpf


title: O1_ATlo

value: bone marrow

value: purified hematopoietic stem cell

value: Old

value: ATlo (GFPhi)


title: 207675480011_R06C03


title: MBD-2-d7 biol rep2 7dpf

value: mbd5 Knock out


title: O1_AThi

value: AThi (GFPlo)

value: steady state isolation


title: 0.1uM_Prochloraz_A549, A_379

description:
A_379
A549_Prochloraz_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: A549 cells treated with 0.1uM Prochloraz


title: 207675480004_R15C02


title: MBD-1-d7 biol rep1 7dpf

value: whole larvae


title: 207675480004_R07C03

value: Raji


title: AB-2-d7 biol rep2 7dpf


title: WSU-FSCCL IgG4 replicate 3

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

country: United Kingdom

institute: University College London

data_processing:
RNA-seq analysis  was performed on LatchBio. First, as a pre-processing step, FastQC was used to confirm per base sequence quality giving the per-site distribution over the length of the read and sequence duplication levels. TrimGalore was used to remove Illumina sequencing adaptors, followed by transcript “pseudo-alignment” using salmon. Tximport was used to convert mapped transcripts into gene-level read counts.
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet containing log2-normalised read counts of the individual samples

molecule: polyA RNA

source_name: B Lymphoma

growth_protocol: WSU-FSCCL cells were cultured in RPMI (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1X MEM non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 50µM 2-mercaptoethanol (Sigma Aldrich), 100U/ml penicillin and 100µg/ml streptomycin and maintained at 37°C in humidified incubators with 5% CO2. The cell line was authenticated by STR and tested mycoplasma-free.

extract_protocol:
RNA was isolated from 5x106 sorted WSU-FSCCL IgG+ and IgM+ cells using the RNeasy mini kit (Qiagen, 74004). RNA quality control was performed using a Bioanalyzer (Agilent).
Stranded mRNA libraries were prepared using a KAPA mRNA HyperPrep Kit (Roche)

treatment_protocol: Stable WSU-FSCCL cells expressing Cas9 were established. The WSU-FSCCL Cas9 cells were lentivirally transduced with a dual-targeting sgRNA lentiGuide-mCherry construct to targeting IgM and IgG4 switch regions. mCherry+ IgM+ or mCherry+ IgG+ cells were sorted by flow cytometry.

value: B Lymphoma

value: WSU-FSCCL

value: Class-switching induced by CRISPR/Cas9 targeting of IgM and IgG4 immunoglobulin switch regions

value: Flow sorting for cells expressing surface IgM


title: 207675480004_R13C02


title: 0.0316uM_Prochloraz_A549, A_378

description:
A_378
A549_Prochloraz_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Prochloraz


title: WSU-FSCCL IgG4 replicate 2


title: AB-1-d7 biol rep1 7dpf

value: AB WT


title: 207675480004_R11C02


title: WSU-FSCCL IgG4 replicate 1

value: Flow sorting for cells expressing surface IgG


title: 207675480004_R09C02


title: 0uM_Prochloraz_A549, A_376

description:
A_376
A549_Prochloraz_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM Prochloraz


title: WSU-FSCCL IgM replicate 2


title: 0.316uM_Prochloraz_A549, A_375

description:
A_375
A549_Prochloraz_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Prochloraz


title: UTR-morphants biol rep2  52hpf

value: mbd5 Knock down


title: UTR-morphants biol rep1  52hpf


title: WSU-FSCCL IgM replicate 1


title: 207675480004_R07C02


title: MBD biol rep2  52hpf

value: mbd5 Knock out


title: 207675480004_R05C02


title: 0.316uM_Prochloraz_A549, A_380

description:
A_380
A549_Prochloraz_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.0316uM_Prochloraz_A549, A_373

description:
A_373
A549_Prochloraz_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R03C02


title: MBD biol rep1  52hpf


title: SNR_42, NL disease sample

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x100bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were performed with Illumina BCL2FASTQ v2.19.0
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR 2.6.1c
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: HG38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

source_name: Patient skin biopsy

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen). 100 ng of Total RNA was used to prepare the sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq RNA Access kit following manufacturer's protocols.

value: Patient skin biopsy

value: patient skin tisuse

value: NL disease


title: SNR_46, NL disease sample


title: 0.01uM_Prochloraz_A549, A_377

description:
A_377
A549_Prochloraz_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: tumorigenic breast epithelial cell

value: A549 cells treated with 0.01uM Prochloraz


title: 0.01uM_Prochloraz_A549, A_372

description:
A_372
A549_Prochloraz_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R15C01


title: SNR_41, NL disease sample


title: SNR_40, NL disease sample


title: AB biol rep1 52hpf

value: whole larvae


title: 0uM_Prochloraz_A549, A_371

description:
A_371
A549_Prochloraz_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R14C03


title: 0.1uM_Prochloraz_A549, A_369

description:
A_369
A549_Prochloraz_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Prochloraz


title: SNR_39, NL disease sample


title: 0.1uM_Prochloraz_A549, A_374

description:
A_374
A549_Prochloraz_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: SNR_38, NL disease sample


title: MATR3_rep2.fastq.gz

first: Markus

last: Hafner

address: 50 South Drive

institute: NIAMS/NIH

data_processing:
bcl2fastqused for basecalling. The analyis was performed as described previously using PARalyzer built into the PARpipe  pipeline
Assembly: hg38
Supplementary files format and content: comma separated file
Supplementary files format and content: contails cluster region and conversion event related information

source_name: Kidney

extract_protocol:
Matrin-3 PAR-CLIP method was performed in three biological replicates as described previously (Benhalevy et al., 2017; Hafner et al., 2010).
Small RNA cDNA library preparation protocol was performed as described in Benhalevy et al., (2017).

value: Kidney

tag: antibody


title: 0.0316uM_Prochloraz_A549, A_368

description:
A_368
A549_Prochloraz_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: MATR3_rep3.fastq.gz


title: 207675480011_R11C01


title: SNR_37, NL disease sample


title: 207675480011_R09C01


title: 207675480004_R01C02


title: SNR_36, NL disease sample


title: 0.316uM_Prochloraz_A549, A_370

description:
A_370
A549_Prochloraz_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: AMB8_S8

city: Oklahoma City

first: Willard

last: Freeman

state: OK

address: 834 NE 13th St

department: GHD

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent)
Reads were aligned against the Panu 3.0 build of the olive baboon genome
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30. Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation
Normalization was performed with the DESeq algorithm. Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable
For statistical analysis of differential expression, a two-tailed t-test and a Benjamini-Hochberg Multiple Testing Correction was used.
Assembly: Panu 3.0
Supplementary files format and content: txt files, raw data for each sample

organism: Papio anubis

source_name: Hippocampus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 25 ng of total RNA was used for the construction of sequencing libraries.
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 25 ng of total RNA for the preparation of strand-specific sequencing libraries from each RNA sample, according to manufacturer's instructions

value: Hippocampus

tag: library prerp_kit


title: AMB9_S9

value: NEBNext Ultra II Directional Library Prep Kit for Illumina


title: 0.01uM_Prochloraz_A549, A_367

description:
A_367
A549_Prochloraz_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: AB biol rep2  52hpf


title: SNR_32, NL disease sample


title: 207675480011_R07C01

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).


title: AMB7_S7


title: 207675480011_R05C01


title: 0.316uM_Prochloraz_A549, A_365

description:
A_365
A549_Prochloraz_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads


title: 0.1uM_Prochloraz_A549, A_364

description:
A_364
A549_Prochloraz_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: SNR_29, NL disease sample


title: 207675480011_R03C01


title: AMB6_S6


title: 207675480011_R13C01


title: 0.0316uM_Prochloraz_A549, A_363

description:
A_363
A549_Prochloraz_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Prochloraz


title: MATR3_rep1.fastq.gz


title: 207675480011_R04C03

value: Jurkat


title: 0.01uM_Prochloraz_A549, A_362

description:
A_362
A549_Prochloraz_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: SNR_14, NL disease sample


title: AMB5_S5


title: 207675480011_R01C01


title: AMB4_S4


title: 0uM_Prochloraz_A549, A_366

description:
A_366
A549_Prochloraz_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0uM_Prochloraz_A549, A_361

description:
A_361
A549_Prochloraz_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Prochloraz_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: SNR_13, NL disease sample


title: 207675480004_R16C01


title: AMB3_L1000


title: SNR_04, NL disease sample


title: 207675480004_R14C01


title: AMB10_S10


title: SNR_03, NL disease sample


title: 10uM_DNCB_A549, A_360

description:
A_360
A549_DNCB_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 10uM DNCB


title: SNR_24, NL disease sample


title: 207675480004_R12C01


title: SNR_02, NL disease sample


title: 1uM_DNCB_A549, A_358

description:
A_358
A549_DNCB_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM DNCB


title: 3.16uM_DNCB_A549, A_359

description:
A_359
A549_DNCB_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM DNCB


title: 8308-OXBS-SRO_S14

data_processing:
Prior to alignment, paired-end reads were adaptor-trimmed and filtered using Trimmomatic 0.35. End-trimming removed leading and trailing bases with Q-score<25, cropped 4 bases from the start of the read, dropped reads less than 25 bases long, and dropped reads with average Q-score<25
Alignment of trimmed bisulfite converted sequences was carried out using Bismark 0.16.3 with Bowtie 2 against the Papio anubis reference genome (Panu 3.0).
Binary alignment maps (BAMs) were de-duplicated using Bismark. Methylation call percentages for each CpG and non-CpG (CH) site within the genome were calculated by dividing the methylated counts over the total counts for that site in the oxidative bisulfite - converted libraries (OXBS)
Genome-wide CpG and CH methylation levels were calculated separately. Hydroxymethylation levels in CpG (hmCG) and CH (hmCH) contexts were calculated by subtracting call levels from the oxidative bisulfite-converted (OXBS) libraries from the bisulfite-converted (BS) libraries
BAM files generated by MethylSeq (Basespace, Illumina) were run through MethylKit in R to generate context-specific (CpG/CH) coverage text files.
Bisulfite conversion efficiency for C, mC, and hmC was estimated using CEGX spike-in control sequences. Untrimmed fastq files were run through CEGX QC v0.2, which output a fastqc_data.txt file containing the conversion mean for C, mC, and hmC.
Assembly: Panu 3.0
Supplementary files format and content: txt files, raw data for each sample

extract_protocol:
The DNA was extracted by Qiagen spin columns and 250ng was oxidized or not and then bisulfite converted with the Tecan Ultralow Methyl-Seq library preparation(#9513-A01; Tecan Genomics).
200 ng of  DNA aliquots per sample, one was oxidized and then bisulfite- converted and the other only bisulfite-converted with the True Methyl oxBS module (NuGEN) with desulfonation and purification
Whole genome oxidative bisulfidate sequencing

tag: library prep

value: Tecan Ultralow Methyl-Seq  with TrueMethyl oxBS module


title: 207675480004_R08C01


title: SNR_01, NL disease sample

value: Patient skin biopsy


title: 207675480004_R10C01


title: 8308-BS-SRO_S4

value: Tecan Ultralow Methyl-Seq


title: 5904-OXBS-SRO_S13


title: 0.316uM_DNCB_A549, A_357

description:
A_357
A549_DNCB_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM DNCB


title: 207675480004_R06C01


title: 0.1uM_DNCB_A549, A_356

description:
A_356
A549_DNCB_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM DNCB


title: SNR_49, control

value: patient skin tisuse

value: Ctrl


title: 5904-BS-SRO_S3


title: SNR_48, control


title: 3909-OXBS-SRO_S18


title: 10uM_DNCB_A549, A_355

description:
A_355
A549_DNCB_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480004_R04C01


title: SNR_47, control


title: 3909-BS-SRO_S8


title: 207675480004_R02C01


title: 207675480016_R16C02

value: HeLa


title: SNR_22, control


title: SNR_17, control


title: 3406-OXBS-SRO_S20


title: 207675480016_R15C02


title: 3406-BS-SRO_S10


title: 0.316uM_DNCB_A549, A_352

description:
A_352
A549_DNCB_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.1uM_DNCB_A549, A_351

description:
A_351
A549_DNCB_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480016_R13C02


title: 3304-OXBS-SRO_S17


title: 3304-BS-SRO_S7


title: 10uM_DNCB_A549, A_350

description:
A_350
A549_DNCB_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: kyse520

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

data_processing:
Samples were sequenced on an Illumina HiSeq4000 with single 50bp reads at 100x106 reads per sample.
Data went through quality control using FastQC.
Assembly: Reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1, and annotated with Gencode v32.
Supplementary files format and content: Raw counts
Supplementary files format and content: DESeq2 vst values log2 normalized

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA universal kit (Qiagen, Hilden, Germany). NanoDrop (Thermo Fisher, Waltham, MA) was used to measure RNA concentration. Biopsies were sent for RNA sequencing in case tumor purity was ≥ 30% and RNA concentration was above 20 ng/µL.
Library preparation was performed using Total RNAlibrary prep RiboErase (Roche, Basel, Switzerland).

value: esophageal squamous cell carcinoma


title: 207675480016_R11C02


title: 207675480016_R09C02


title: 1uM_DNCB_A549, A_348

description:
A_348
A549_DNCB_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480016_R07C02


title: oe33

value: esophageal adenocarcinoma


title: 2608-BS-SRO_S2

value: Hippocampus


title: 3.16uM_DNCB_A549, A_354

description:
A_354
A549_DNCB_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: oe19


title: 2608-OXBS-SRO_S12


title: 207675480016_R05C02


title: 13509-OXBS-SRO_S19


title: 0.316uM_DNCB_A549, A_347

description:
A_347
A549_DNCB_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: flo1


title: 0.1uM_DNCB_A549, A_346

description:
A_346
A549_DNCB_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: oe21


title: 207675480016_R03C02


title: 10uM_DNCB_A549, A_345

description:
A_345
A549_DNCB_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 13509-BS-SRO_S9


title: 207675480016_R01C02


title: 289b


title: kyse410


title: 10310-OXBS-SRO_S11


title: 3.16uM_DNCB_A549, A_344

description:
A_344
A549_DNCB_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207675480011_R02C03


title: 3.16uM_DNCB_A549, A_349

description:
A_349
A549_DNCB_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 081r


title: 10310-BS-SRO_S1


title: 207675480004_R15C01


title: 1uM_DNCB_A549, A_343

description:
A_343
A549_DNCB_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 058b


title: 1uM_DNCB_A549, A_353

description:
A_353
A549_DNCB_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 10209-OXBS-SRO_S15


title: 037m


title: 207675480004_R13C01


title: 0.316uM_DNCB_A549, A_342

description:
A_342
A549_DNCB_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.1uM_DNCB_A549, A_341

description:
A_341
A549_DNCB_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 031m


title: SS4

city: Providence

first: Madison

last: Silvia

state: Rhode Island

address: 185 Meeting St

department: MCB

institute: Brown University

data_processing:
Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 [2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and generate a better mapping result than other non-splice mapping tools
FeatureCounts [4] v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene
Assembly: L. variegatus assembly v3.0
Supplementary files format and content: raw, fpkm counts for each sample

organism: Lytechinus variegatus

source_name: Secondary Spines

extract_protocol:
Spines were immersed in TriZol and RNA was extracted following the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library [1]. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification(Figure 2.A). For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount

value: Secondary Spines

value: wild type


title: 007b


title: SS3


title: amc-446-eac

source_name: Primary Tumor Biopsy

value: Primary Tumor Biopsy

value: tumor

value: male

tag: age at_diagnosis

tag: differentiation grade

value: unknown


title: 0.01uM_DNCB_A549, A_339

description:
A_339
A549_DNCB_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

tag: cell line

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.01uM DNCB


title: 207675480004_R07C01

source_name: Human cell line DNA

tag: tissue


title: SS2


title: amc-357-eac

tag: cell type


title: 207675480004_R05C01


title: amc-350-eac


title: 0.00316uM_DNCB_A549, A_338

description:
A_338
A549_DNCB_0.00316uM_Rep8
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM DNCB


title: SS1


title: PS4

source_name: Primary Spines

value: Primary Spines


title: amc-349-eac


title: 10209-BS-SRO_S5

value: Tecan Ultralow Methyl-Seq


title: 0uM_DNCB_A549, A_336

description:
A_336
A549_DNCB_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM DNCB


title: 0.0316uM_DNCB_A549, A_335

description:
A_335
A549_DNCB_0.0316uM_Rep7
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM DNCB


title: 207675480004_R01C01

value: HeLa


title: PS3


title: PS2


title: 207675480004_R11C01


title: amc-329-eac


title: 207854510042_R15C03

source_name: Human primary cell DNA

value: skin


title: PS1


title: 207675480004_R09C01


title: 0.01uM_DNCB_A549, A_334

description:
A_334
A549_DNCB_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.0316uM_DNCB_A549, A_340

description:
A_340
A549_DNCB_0.0316uM_Rep8
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-328-esc


title: 207854510042_R11C03


title: 0.00316uM_DNCB_A549, A_333

description:
A_333
A549_DNCB_0.00316uM_Rep7
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: MATR3 KO #5

first: Stefan

last: Muljo

state: MD

address: 10 Center Drive

institute: NIH, NIAID

data_processing:
MinKNOW software was used to basecall reads and generate fast5 and fastq files.
Reads were mapped to hg38 using minimap2 (PMID: 29750242) using the following parameters:- x map-ont -secondary=no -ax splice –uf .
The resulting bam files were then filtered for mapping quality and unique mapping using samtools view -F 256 -q 20, and converted to RPM-normalized bigwig files.
The filtered bam file were used along with Gencode v 33 as input to subread’s (PMID: 23558742) (version 2.0.1) feature count (parameters: -L -t exon -g gene_id) to quantify gene level expression. Differential expression was determined by DESeq2 version 1.22.2 (PMID: 25516281).
Assembly: hg38
Supplementary files format and content: Excel file contains Raw Counts, DESeq normalized counts, and DESeq differential expression results comparing the MATR3 KO to the HAP1 WT samples.

growth_protocol: HAP1 cells were cultured in IMDM medium (Quality Biological, cat# 112-035-101) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (Gibco, cat# 26170-043), 100 U/mL penicillin, 100 µg/mL streptomycin (Gibco, cat# 15140-122), at 37° C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was isolated using RNAzol (Sigma, cat#R4533-100ML) per manufacturer’s instruction. RNA was quantified with Qubit RNA HS BR Assay Kit (Thermo Fisher Scientific, cat#Q10210??) and Qubit 4 Fluorimeter according to manufacturer’s instruction. RNA integrity was verified with HS RNA Kit (15NT nt) on the 5200 Fragment Analyzer (Agilent Technologies, cat# DNF-472-500) per manufacturer’s protocol.
The ONT PCR-cDNA sequencing kit (Oxford Nanopore Technologies, cat# SQK PCS-109) was used for library preparation per manufacturer’s instructions. For each sample, 50 ng of input total RNA was used. Libraries were sequenced on the MinION Mk1C using R9.4.1 flow cells (Oxford Nanopore Technologies, cat#??)

treatment_protocol: MATR3 KO clones 1 and 5 were purchased from Horizon Discovery (cat# HZGHC007500c001, HZGHC007500c004 and HZGHC007500c005) alongside Wild Type control (cat# C631_31144, batch 36899 - Clone #4)

value: KBM-7 (CML)-derived near-haploid cell line

value: MATR3 knockout


title: amc-327-eac

value: not determined

value: nd


title: 0.001uM_DNCB_A549, A_337

description:
A_337
A549_DNCB_0.001uM_Rep4
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.001uM DNCB


title: 207675480004_R03C01

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia


title: MATR3 KO #1


title: amc-323-eac

value: Primary Tumor Biopsy

value: tumor


title: 207854510042_R08C03


title: 207854510042_R06C02


title: amc-322-eac

value: female


title: HAP1 WT #4 rep2

value: Wild Type